Pictures, please

Some pictures of your problem children might help us to help you.  What follows is some general advice:

Start with the trucks, always.  Get those sorted, including any modifications to the trucks and the bolsters, and then install the couplers to work with the trucks.  For starters, when cutting off the truck mounted couplers, remove everything all the way back to the bolster - ideally the truck should be symmetrical when you're done, but practically, just removing as much as possible is the general idea.  Make sure you ream the bearings.  Not all trucks use the same length axle, and a reamer can help with a truck which is a little tight.  It will also do wonders for the rolling quality of the trucks once you add metal wheels.

Sometimes (especially in the case of box cars) it's easier to leave the bolsters alone and move the car floor up into the body, if you want the car to ride lower.  For the cars with snap in trucks, when you remove some of the bolster the trucks can get loose.  They'll still ride well enough, but they hang down when you're handling them, and it can be hard to get them on the rails.  The solution is to add some material to the top side of the floor if possible.  I usually don't bother.

If you decide to replace the trucks, I like to rebuild the mounting posts using a variety of sizes of styrene tube, and a 2-56 drill and tap set.  A couple sizes are usually sufficient, and one piece of each will do a LOT of cars, since you're only using about 1/2" per car.

Once you have the truck mounting and ride height figured out, then you can figure out how to mount the couplers.  I definitely would not suggest gluing them in place until you're sure that you have them right.  As a general rule (but by no means always) the bottom of the coupler box should be even with the bottom of the body bolster.  At the very least, that's usually a good place to start.

The key to solving a multi-faceted problem is to work on only one thing at a time.  As I said, I always start with the trucks.  If you start with the couplers, then you're stuck having to modify the trucks to suit.  Remember to work one one item and then leave it alone after that.

Quick question, Ken and

Quick question, Ken and thanks for the help.

If I start with the trucks how will I know when they are sitting at the correct height?  I started with the couplers because I wanted to align them to the gage.

My biggest problem was gluing them in before I had everything set up.  If i had waited, I could reposition them now.

Like i said, I'm not too upset (other then making such a stupid move).  I have about 2 or three of each type car to redo the set for Daniel (My grandson).  I'm also learning a lot about plastics and glue.

I do want to convert the snap in trucks.  I was gonna do that but I don't have any suitable material on hand.  My LHS is too high priced for that sort of stuff so I need to get it on line.  I saw  video earlier on Youtube that showed a guy dissolving sprues in nail polish remover and it made like a paste he used to fill holes.  Looks like it might work in this case.  I threw some sprues that the gear boxes came on ib a small jar with some nail polish remover...   We'll see what happens, lol.

I'll get some pics tonight.

It depends on your goal

If all you want is the fastest, easiest way to get a car running reliably, then starting with the couplers might make sense in a few cases.  However, since the ride height is such an important part of how a car looks, it is often better from a prototypical standpoint to address the trucks first.  Also, it is often easier to change the coupler height, compared to the truck mounting design.  Thus, it's often both easier and better looking if you start with the trucks first, and adjust the couplers to suit.

Plastic filler is just plastic which has been dissolved in some sort of solvent.  However, unless you're unable to find anything better, I'd stay away from things like nail polish remover.  The good stuff has acetone in it, but it's hardly pure.  It's both cheaper and more effective to buy the acetone, lacquer thinner, or MEK straight from the hardware store.  I'm partial to MEK, and I know a lot of modelers who swear by lacquer thinner.  Acetone is less useful for styrene, but it will work, and it will bond acrylics like Plexiglas as well.

In any case, I don't suggest that you fill the boles in the body with putty of any kind, for three main reasons.  It will shrink considerably, and take forever to dry enough to drill and tap properly.  It will probably not be as strong as solid styrene.  It will not be easy to get the new truck mounting hole perfectly located.  Gluing in styrene tube solves all of those problems, and it also allows you to make a raised post on which the truck can rotate.  Some trucks are designed for that, some are not, but it gives you the ability to built to suit your trucks.

I thought a picture might be handy, to show some of the conversions I've done:

You can see the cars with their respective trucks, and the modifications made.  For the gon, I made new styrene truck mounting posts which also serve to locate the floor.  After gluing them in and letting them cure, I drilled and taped them for 2-56 screws, and used Tichy trucks.  Both of the box cars are running on modified and weathered snap in trucks which originally had couplers mounted on them.  Notice that the new coupler boxes butt up against the body bolsters, which meant that the trucks had to be trimmed to ensure that nothing extends beyond the side of the bolster.  Since the bolster and coupler box are flush with each other, the truck can still swivel.  Notice that in both cases, the bolsters are not modified.  I adjusted the ride height by setting the car floors up into the bodies a little further.  Also notice the styrene pads which I glued in place to get the couplers at the correct height.  Not as easily visible are the notches in the car ends to clear the boxes.  While not always prototypical, I often resort to them in order to get that really low-riding look of older box cars.

[edit]

I thought I'd share a photo of the cars on the layout, to show what they look like in service:

And a close-up of the two box cars:

That loco

First of all, what Model Power loco is it?  If I had to guess, I'd say it's the 0-4-0T, as they're nearly ubiquitous.  My second guess would be a 2-6-0.  Last would be either the 4-6-2 or 2-8-2 which has been sold by Model Power, Mehano, IHC, AHM, and probably others over the years, in differing levels of quality.  Again, a photo might be helpful if you can post one or two.

The larger locos will benefit GREATLY from using the tender wheels to pick up power as well.  This can be done fairly easily (if you have some basic tools and skills) using Kadee coupler centering springs as shown here.  The smaller locos would benefit just as much, but they probably don't have tenders in the first place.

In any case, it sounds like you're going to have to disassemble and clean the mechanism.  hoseeker.net is an excellent resource for drawings and diagrams which will help you.  If you do that the model apart, take it easy, make notes or take photos of every step, and make sure you keep all the parts together in one place.  Most of the inexpensive steam mechanisms I've seen have relatively few parts, so disassembly and reassembly ought to be pretty easy.  Often the hardest part of the process is making sure the wheel wipers are tucked into proper position, since they're sprung to make good contact with the wheels and sometimes want to get trapped in the wrong positions.

I recently completed a similar dismantling and cleaning of an Atlas S1, which had completely stopped working rue to corrosion on the wipers, and wires which had broken at the solder joints.  The solution was a thorough cleaning and careful re-lubrication, and soldering new wires in place of the old ones.  I also used a dab of No-Ox on the backs of the wheels to hopefully prevent future corrosion and maintain better continuity from wheels to wipers.  It's not a difficult job, as long as you're patient and methodical.

Wow, wow, wow, Ken.  Thanks

Wow, wow, wow, Ken.  Thanks so much for all the help.

Ok, I'm gonna make up a list of material, get it and  do this the right way.  The cars are not important but learning to do it right is.

Ok, pictures/  One of the

Ok, pictures/  One of the fleet and a close up of the restricted wheel movement.

Hmmm

I'm afraid that I don't see the problem.  Are the wheels on the gon rubbing against the bottom of the car?  If the problem is the fact that the truck can't turn any farther than shown in the photo, I don't think it's actually a problem unless you're running on 6" radius curves!  I can see one truck on the caboose which is turned sideways, but that ought to be easy enough to fix.

Oops, now I see the photo of the hopper.  Are the bolsters even with the bottoms of the coupler boxes?  If not, try adding a little material to get them both level.  You may have some issues with that hopper, unless you just go ahead and rebuild the bolster to take a screw mounted truck.

I was thinking, you might be able to break the CA joint with a chisel blade or screwdriver used as a wedge.  CA isn't very strong, especially in tension.  You could also encourage it with a little acetone or fingernail polish remover, but be careful because it will also dissolve the car!  Apply a little drop right on the glue joint, work the joint a little, add another drop, and repeat until the joint is broken.

I'd definitely suggest adding wipers to the tender wheels on the engine.  Even if the engine itself had perfect pickup, you'd be increasing the number of wheels picking up power by three times, from 4 to 12.  An 0-4-0 is just about the worst case scenario for reliable pickup and running.

The couplers all line up with

The couplers all line up with gage but the wheels hit the edge of the coupler box.  Yes, the bolster on the car is filed down to the car body in order for it to line up with the coupler gage.  

I was thinking of getting rid of the modified trucks and picking up some of these trucks and changing the wheels.  http://www.ebay.com/itm/280794652181?ssPageName=STRK:MEWAX:IT&_trksid=p3984.m1423.l2649

Gonna try and get the coupler boxes off.  thanks for the hints.  I saw somewhere else that putting them in the freezer over night helps also.

Gona put a list together tonight.

I don't think the problem is as bad as you think

Are you having a problem with that while on the track, or just on the workbench?  I'm asking because normally the trucks will never need to rotate far enough to hit the coupler boxes.  Looking at your photo, it looks like you've got more than enough truck rotation for any reasonable radius curve, and probably for a curve so tight that the cars would never stay coupled anyway.

Those Tichy trucks are pretty nice.  I like them because they're inexpensive and available in a variety of styles.  I do always make sure to ream the bearings and replace the wheels with metal ones.  Remember that if you replace the trucks, you'll have to make some sort of mounting for the new trucks.  The Tichy trucks I've seen are made to fit around a 2-56 screw, with the head fitting neatly inside the truck bolster.  That means you'll need to fill in the hold in the body bolster and drill & tap it.

More thoughts on the loco

I glanced at the drawing (such as it is) on hoseeker of the Model Power 0-4-0 shifter.  It looks like you can remove the two screws holding the bottom cover plate in place, then remove the cover plate and wheels to get access to the wipers.  Check that they are not corroded or bent, and that the wires from the wipers to the motor are intact.  You could completely disassemble the model at this point if you like, or put it back together.

I would go ahead and add the tender wheel wipers on every wheel.  Just make sure that you don't cross your wires anywhere, and solder the leads from the tender directly to the motor, or to any convenient place on the leads from the wipers on the loco.  That should help it become a pretty reliable running little engine.  If you think there's ever a chance the engine will get a DCC decoder, you might want to run the leads from the driver wipers into the tender, and from there back to the motor.  That way it's an easy job to put a decoder in the tender in the future.  However, that may be more work than it's worth at the moment.

Older or inexpensive equipment often needs a little TLC in order to be reliable.  It's not difficult, but it is a necessity, and it's the reason so many modelers are willing to pay premium prices in order to be able to take a model out of the box and run it.  Personally, I enjoy taking these neglected and maligned models and making them run well, and it's definitely the cheaper way to go.  I also think that the skills you're learning will serve you throughout your hobby career.  Too many people don't have any idea how to be their own mechanics, and don't want to.

Yep. gonna take all you

Yep. gonna take all you advice and put it to work.   I'm gonna go over all the couplers 1 more time.   I want to covert them to tichy trucks.   I was also looking to get rid of the plastic 2 56 truck threads and replace them with metal but so far all I've seen do not tell me how big the head is,

I haven't added any weight to these cars yet but they are all 3 or so onces lighter then standard.  I have some 1/4 ounce auto wheel weights and a bottle of Daisy air rifle bb's on the way.  I was watching them go around the track earlier and I think I saw one kind of just tip over.

Anyway, yeah, I like working with these neglected cars also. 

Weight

I super-glue pennies inside boxcars. 11-12 pennies to an ounce depending on wear. It's cheaper than buying A-Line weights.

willie

Ok, I haven't had much time

Ok, I haven't had much time to work on these cars but I did manage to do one.  I took your advice, Ken and made sure the floor height was correct before I did the coupler.  When i did that the coupler needed no adjustment at all.

I filed away the some of the bolster until it rested on the floor height part of the Kadee coupler gauge.  did I do it right?